Source code for dynamo.simulation.evaluation

import numpy as np
from sklearn.metrics import mean_squared_error


[docs]def evaluate(reference, prediction, metric="cosine"): """Function to evaluate the vector field related reference quantities vs. that from vector field prediction. Parameters ---------- reference: `numpy.ndarray` The reference quantity of the vector field (for example, simulated velocity vectors at each point or trajectory, or estimated RNA velocity vector) prediction: `numpy.ndarray` The predicted quantity of the vector field (for example, velocity vectors calculated based on reconstructed vector field function at each point or trajectory, or reconstructed RNA velocity vector) metric: `str` The metric for benchmarking the vector field quantities after reconstruction. Returns ------- res: `float` The score between the reference vs. reconstructed quantities based on the metric. """ if metric == "cosine": true_normalized = reference / np.linalg.norm(reference, axis=1).reshape(-1, 1) predict_normalized = prediction / np.linalg.norm(prediction, axis=1).reshape(-1, 1) res = np.mean(true_normalized * predict_normalized) * prediction.shape[1] elif metric == "rmse": res = mean_squared_error(y_true=reference, y_pred=prediction) return res